In submarine environments, ferromanganese (Fe–Mn) oxides are formed via various processes. Although hydrothermal Fe–Mn oxides are generally valueless as mineral resources because of their low critical metal content, they reflect temporal changes in hydrothermal activity. Metal particles, including native metals, have been observed in hydrothermal Fe–Mn oxides and associated igneous rocks that are extensively distributed in the Sea of Japan. This finding can have significant implications for metal transport in submarine hydrothermal systems. However, the existence of these metal particles requires verification because their thermodynamic coexistence with Mn oxides is challenging and has only been reported by one research team. Here, we show the growth structure and geochemistry of hydrothermal Fe–Mn oxides and volcanic rocks from the Daini-Nishi-Yamato Seamount in the Sea of Japan. The chemical and Nd–Sr isotopic compositions of the volcanic rock indicated that the Daini-Nishi-Yamato Seamount formed through magmatism after back-arc spreading in the Yamato Basin at 10–17 Ma. The hydrothermal Fe–Mn oxides consisted of Ti-rich layers that formed earlier and Ti-poor layers that formed later. The Ti-rich layers precipitated from Ti-rich hydrothermal fluids because of water–rock interactions at higher temperatures during the early stages of hydrothermal activity. During the late stages of hydrothermal activity, Ti-poor layers formed, likely because of a decrease in the temperature of the water–rock interactions and/or the depletion of Ti in the host rocks. However, unlike in previous studies, metal particles such as Ag and rare earth elements were not detected in our samples, which were impregnated with resin to prevent contamination during the polishing process. These results strongly suggest that the metal particles reported in the previous studies were contaminants.